Effects of mitochondrial haplogroups and variants on anthracycline associated cardiomyopathy
Jeremy Leipzig & Marijana Vukovic
3/7/2017
MitoChip and MiSeq analysis
97 subjects were run through the Illumina MitoChip v2. Calls were processed using ReseqChip to obtain consensus sequences. These were processed through Mitomaster to obtain variants and Haplogroup calls (via Haplogrep).
96 subjects were sequenced on an Illumina MiSeq and aligned by CAG using bwa-mem to the g1k_v37 reference. Samtools/bcftools was used to create a consensus sequence for reads mapping to MT. These sequences were also processed through Mitomaster.
7 subjects were run on both platforms.
Population structure
Initial findings
Concordance of sequence and microarray data
Sequence and microarray microhaplogroups were identical between the 7 samples run on both platforms
Duplicate microarray samples were removed for the remainder for the analysis.
| Regno | cnt | samples | sources | mhaps |
|---|---|---|---|---|
| 821630 | 2 | 821630, Mito_AML1031_PT1_F09_821630 | seq, chip | U5a1a1d, U5a1a1d |
| 822655 | 2 | 822655, Mito_AML1031_PT1_B02_822655 | seq, chip | C, C |
| 823157 | 2 | 823157, Mito_AML1031_PT1_H09_823157 | seq, chip | K1a1b1a, K1a1b1a |
| 825090 | 2 | 825090, Mito_AML1031_PT1_C10_825090 | seq, chip | H1, H1 |
| 828528 | 2 | 828528, Mito_AML1031_PT1_E03_828528 | seq, chip | H5, H5 |
| 829368 | 2 | 829368, Mito_AML1031_PT1_E07_829368 | seq, chip | C, C |
| 830330 | 2 | 830330, Mito_AML1031_PT1_C11_830330 | seq, chip | H3a1, H3a1 |
Loci
A total of 953 loci witnessed variants in at least one subject.
A word of caution
rCRS is a somewhat arbitrary reference with microhaplogroup H2a2a1. Variants from the rCRS do not imply deleteriousness, and in many cases reference alleles are risk factors for disease or other non-optimal outcomes. It is just as important to weight “protective variants” equally.
Variants by genbank frequency
Mitomaster computes frequency of each variant in its corpus of 30,589 GenBank sequences. 
Variants by haplogroup frequency
Mitomaster also computes frequency within minor haplogroups. Frequencies near 100% are likely haplogroup-defining variants 
625 of the variants are very rare (<1%) could be Mitochip artefacts, especially if they appear in more than one subject. Others are more common than not, and reflect the oddity of rCRS as a reference.
The breakdown of macro haplogroups
Why are there so many Asians when that is not a self-reporting group? Here is the breakdown of Asian haplogroups:
| macrohaplogroup | count |
|---|---|
| A | 13 |
| B | 8 |
| C | 9 |
| D | 5 |
| M | 3 |
| N | 1 |
What is the concordance with SVM PCA-component classified by Hapmap populations
These calls were made using the SVM’s trained on HapMap and the following breakdown:
EUR = CEU + TSI
AFR = ASW + LWK + MKK + YRI
MEX = MXLSee https://github.research.chop.edu/vujkovicm/aplenc_gwas/blob/master/R/pop_strat.R for the code.
The prevalance of A haplogroups associated with Amerindian populations in Mexico is historically consistent. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051415/
Autosomal population background
Classification
Three principal components from population-defining SNPs were provided as courtesy by CAG.
The first two PCs against self reported ethnicity: 
Left ventricular systolic dysfunction
Distribution
Cannot justify using parametric tests.
Macrohaplogroup analysis
| macrohaplogroup | cnt | mean_lvsd |
|---|---|---|
| N | 1 | 0.0000000 |
| HV | 5 | 0.6000000 |
| K | 13 | 0.7307692 |
| L0 | 4 | 0.7500000 |
| A | 13 | 0.7692308 |
| J | 15 | 0.9000000 |
| L1 | 4 | 1.0000000 |
| B | 8 | 1.1250000 |
| T | 16 | 1.1875000 |
| H | 56 | 1.2410714 |
| I | 4 | 1.2500000 |
| D | 5 | 1.4000000 |
| U | 16 | 1.4062500 |
| W | 1 | 1.5000000 |
| C | 9 | 1.6666667 |
| L3 | 5 | 1.9000000 |
| L2 | 1 | 3.0000000 |
| M | 3 | 3.0000000 |
| R | 1 | 3.0000000 |
| X | 2 | 3.0000000 |
| V | 4 | NA |
Linear model
##
## Call:
## lm(formula = lvsd ~ macrohaplogroup, data = cpdf)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.6667 -0.9000 -0.1875 0.7589 2.8125
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.75000 0.56969 1.317 0.1898
## macrohaplogroupL1 0.25000 0.80566 0.310 0.7567
## macrohaplogroupL2 2.25000 1.27386 1.766 0.0792 .
## macrohaplogroupL3 1.15000 0.76431 1.505 0.1343
## macrohaplogroupA 0.01923 0.65146 0.030 0.9765
## macrohaplogroupB 0.37500 0.69772 0.537 0.5917
## macrohaplogroupC 0.91667 0.68468 1.339 0.1825
## macrohaplogroupD 0.65000 0.76431 0.850 0.3963
## macrohaplogroupM 2.25000 0.87021 2.586 0.0106 *
## macrohaplogroupN -0.75000 1.27386 -0.589 0.5568
## macrohaplogroupHV -0.15000 0.76431 -0.196 0.8447
## macrohaplogroupH 0.49107 0.58968 0.833 0.4062
## macrohaplogroupI 0.50000 0.80566 0.621 0.5357
## macrohaplogroupJ 0.15000 0.64116 0.234 0.8153
## macrohaplogroupK -0.01923 0.65146 -0.030 0.9765
## macrohaplogroupR 2.25000 1.27386 1.766 0.0792 .
## macrohaplogroupT 0.43750 0.63693 0.687 0.4931
## macrohaplogroupU 0.65625 0.63693 1.030 0.3044
## macrohaplogroupV 0.41667 0.87021 0.479 0.6327
## macrohaplogroupW 0.75000 1.27386 0.589 0.5568
## macrohaplogroupX 2.25000 0.98672 2.280 0.0239 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.139 on 164 degrees of freedom
## (1 observation deleted due to missingness)
## Multiple R-squared: 0.1548, Adjusted R-squared: 0.05169
## F-statistic: 1.502 on 20 and 164 DF, p-value: 0.08673Do the PCA’s based on the microarrays help?
##
## Call:
## lm(formula = lvsd ~ macrohaplogroup + pca1 + pca2 + pca3, data = cpdf)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.6451 -0.8854 -0.1832 0.7770 2.7870
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.58820 0.64384 0.914 0.3623
## macrohaplogroupL1 0.18828 0.93498 0.201 0.8407
## macrohaplogroupL2 2.16806 1.37375 1.578 0.1165
## macrohaplogroupL3 1.07574 0.92999 1.157 0.2491
## macrohaplogroupA 0.06747 0.70701 0.095 0.9241
## macrohaplogroupB 0.23737 0.74730 0.318 0.7512
## macrohaplogroupC 0.87464 0.75315 1.161 0.2472
## macrohaplogroupD 0.50636 0.87655 0.578 0.5643
## macrohaplogroupM 2.09012 0.94927 2.202 0.0291 *
## macrohaplogroupN -0.51965 1.34086 -0.388 0.6989
## macrohaplogroupHV 0.06500 0.85661 0.076 0.9396
## macrohaplogroupH 0.69502 0.69466 1.001 0.3186
## macrohaplogroupI 0.72554 0.90056 0.806 0.4216
## macrohaplogroupJ 0.35143 0.74399 0.472 0.6373
## macrohaplogroupK 0.19255 0.75819 0.254 0.7998
## macrohaplogroupR 2.30424 1.32223 1.743 0.0833 .
## macrohaplogroupT 0.65549 0.74684 0.878 0.3814
## macrohaplogroupU 0.85483 0.73829 1.158 0.2486
## macrohaplogroupV 0.58175 0.91903 0.633 0.5276
## macrohaplogroupW 0.96474 1.33748 0.721 0.4718
## macrohaplogroupX 2.47013 1.06426 2.321 0.0215 *
## pca1 -15.04692 38.90261 -0.387 0.6994
## pca2 15.18466 17.28941 0.878 0.3811
## pca3 -2.44772 12.08871 -0.202 0.8398
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.147 on 161 degrees of freedom
## (1 observation deleted due to missingness)
## Multiple R-squared: 0.1597, Adjusted R-squared: 0.03969
## F-statistic: 1.331 on 23 and 161 DF, p-value: 0.1553Nope.
All-by-all haplogroups kruskal-wallis
##
## Kruskal-Wallis rank sum test
##
## data: lvsd by macrohaplogroup
## Kruskal-Wallis chi-squared = 26.875, df = 20, p-value = 0.1388Due to high variance, no macro haplogroup is significantly different
Haplogroup (letter-number-letter) analysis
| haplogroup | mean_lvsd |
|---|---|
| A2d | 0.0000000 |
| A2k | 0.0000000 |
| B2h | 0.0000000 |
| D1 | 0.0000000 |
| H14b | 0.0000000 |
| H1g | 0.0000000 |
| H2 | 0.0000000 |
| H27a | 0.0000000 |
| H31 | 0.0000000 |
| H3v | 0.0000000 |
| H3y | 0.0000000 |
| H5b | 0.0000000 |
| H7a | 0.0000000 |
| H82 | 0.0000000 |
| HV5 | 0.0000000 |
| HV6 | 0.0000000 |
| I1 | 0.0000000 |
| J2b | 0.0000000 |
| K1 | 0.0000000 |
| K1a | 0.0000000 |
| K2a | 0.0000000 |
| N1b | 0.0000000 |
| T2d | 0.0000000 |
| T2f | 0.0000000 |
| U4b | 0.0000000 |
| A2 | 0.2500000 |
| L1c | 0.3333333 |
| T2b | 0.4166667 |
| H1e | 0.5000000 |
| L0a | 0.7500000 |
| J1c | 0.8500000 |
| A2o | 1.0000000 |
| A2u | 1.0000000 |
| B2a | 1.0000000 |
| B4c | 1.0000000 |
| C1b | 1.0000000 |
| D1d | 1.0000000 |
| D5b | 1.0000000 |
| H47 | 1.0000000 |
| H4a | 1.0000000 |
| HV | 1.0000000 |
| I2d | 1.0000000 |
| I4a | 1.0000000 |
| U2e | 1.0000000 |
| H1b | 1.1000000 |
| H5a | 1.1000000 |
| K1c | 1.1666667 |
| H1a | 1.1875000 |
| U5a | 1.2142857 |
| J1b | 1.2500000 |
| L3d | 1.2500000 |
| B2 | 1.3333333 |
| H16b | 1.3333333 |
| A2a | 1.4000000 |
| H1y | 1.5000000 |
| H2a | 1.5000000 |
| U6a | 1.5000000 |
| W | 1.5000000 |
| B4b | 2.0000000 |
| D4b | 2.0000000 |
| H1 | 2.0000000 |
| H11a | 2.0000000 |
| H6a | 2.0000000 |
| K1b | 2.0000000 |
| K2b | 2.0000000 |
| L3b | 2.0000000 |
| M71a | 2.0000000 |
| U3a | 2.0000000 |
| U5b | 2.0000000 |
| T1a | 2.0833333 |
| C | 2.5000000 |
| C1c | 2.5000000 |
| L3e | 2.5000000 |
| D4j | 3.0000000 |
| H15a | 3.0000000 |
| H24a | 3.0000000 |
| H3 | 3.0000000 |
| H5 | 3.0000000 |
| I2 | 3.0000000 |
| L1b | 3.0000000 |
| L2a | 3.0000000 |
| M7b | 3.0000000 |
| R5a | 3.0000000 |
| X2c | 3.0000000 |
| X2e | 3.0000000 |
| H3a | 4.0000000 |
| M5a | 4.0000000 |
| T1 | 4.0000000 |
| V | NA |
Linear model
##
## Call:
## lm(formula = lvsd ~ haplogroup, data = cpdf)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.0000 -0.3333 0.0000 0.3333 2.1500
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.25000 0.51069 0.490 0.62558
## haplogroupA2a 1.15000 0.68516 1.678 0.09651 .
## haplogroupA2d -0.25000 1.14193 -0.219 0.82717
## haplogroupA2k -0.25000 1.14193 -0.219 0.82717
## haplogroupA2o 0.75000 1.14193 0.657 0.51289
## haplogroupA2u 0.75000 1.14193 0.657 0.51289
## haplogroupB2 1.08333 0.78009 1.389 0.16813
## haplogroupB2a 0.75000 0.88453 0.848 0.39860
## haplogroupB2h -0.25000 1.14193 -0.219 0.82717
## haplogroupB4b 1.75000 1.14193 1.532 0.12869
## haplogroupB4c 0.75000 1.14193 0.657 0.51289
## haplogroupC 2.25000 0.88453 2.544 0.01256 *
## haplogroupC1b 0.75000 0.68516 1.095 0.27641
## haplogroupC1c 2.25000 0.88453 2.544 0.01256 *
## haplogroupD1 -0.25000 1.14193 -0.219 0.82717
## haplogroupD1d 0.75000 1.14193 0.657 0.51289
## haplogroupD4b 1.75000 1.14193 1.532 0.12869
## haplogroupD4j 2.75000 1.14193 2.408 0.01794 *
## haplogroupD5b 0.75000 1.14193 0.657 0.51289
## haplogroupH1 1.75000 0.72222 2.423 0.01726 *
## haplogroupH11a 1.75000 0.72222 2.423 0.01726 *
## haplogroupH14b -0.25000 1.14193 -0.219 0.82717
## haplogroupH15a 2.75000 1.14193 2.408 0.01794 *
## haplogroupH16b 1.08333 0.78009 1.389 0.16813
## haplogroupH1a 0.93750 0.62546 1.499 0.13718
## haplogroupH1b 0.85000 0.68516 1.241 0.21778
## haplogroupH1e 0.25000 0.88453 0.283 0.77807
## haplogroupH1g -0.25000 0.88453 -0.283 0.77807
## haplogroupH1y 1.25000 1.14193 1.095 0.27641
## haplogroupH2 -0.25000 1.14193 -0.219 0.82717
## haplogroupH24a 2.75000 1.14193 2.408 0.01794 *
## haplogroupH27a -0.25000 1.14193 -0.219 0.82717
## haplogroupH2a 1.25000 0.78009 1.602 0.11236
## haplogroupH3 2.75000 1.14193 2.408 0.01794 *
## haplogroupH31 -0.25000 0.88453 -0.283 0.77807
## haplogroupH3a 3.75000 1.14193 3.284 0.00143 **
## haplogroupH3v -0.25000 1.14193 -0.219 0.82717
## haplogroupH3y -0.25000 1.14193 -0.219 0.82717
## haplogroupH47 0.75000 1.14193 0.657 0.51289
## haplogroupH4a 0.75000 1.14193 0.657 0.51289
## haplogroupH5 2.75000 1.14193 2.408 0.01794 *
## haplogroupH5a 0.85000 0.68516 1.241 0.21778
## haplogroupH5b -0.25000 1.14193 -0.219 0.82717
## haplogroupH6a 1.75000 0.88453 1.978 0.05074 .
## haplogroupH7a -0.25000 1.14193 -0.219 0.82717
## haplogroupH82 -0.25000 1.14193 -0.219 0.82717
## haplogroupHV 0.75000 0.78009 0.961 0.33875
## haplogroupHV5 -0.25000 1.14193 -0.219 0.82717
## haplogroupHV6 -0.25000 1.14193 -0.219 0.82717
## haplogroupI1 -0.25000 1.14193 -0.219 0.82717
## haplogroupI2 2.75000 1.14193 2.408 0.01794 *
## haplogroupI2d 0.75000 1.14193 0.657 0.51289
## haplogroupI4a 0.75000 1.14193 0.657 0.51289
## haplogroupJ1b 1.00000 0.72222 1.385 0.16938
## haplogroupJ1c 0.60000 0.60425 0.993 0.32322
## haplogroupJ2b -0.25000 1.14193 -0.219 0.82717
## haplogroupK1 -0.25000 0.88453 -0.283 0.77807
## haplogroupK1a -0.25000 0.78009 -0.320 0.74930
## haplogroupK1b 1.75000 1.14193 1.532 0.12869
## haplogroupK1c 0.91667 0.78009 1.175 0.24287
## haplogroupK2a -0.25000 0.88453 -0.283 0.77807
## haplogroupK2b 1.75000 0.88453 1.978 0.05074 .
## haplogroupL0a 0.50000 0.72222 0.692 0.49041
## haplogroupL1b 2.75000 1.14193 2.408 0.01794 *
## haplogroupL1c 0.08333 0.78009 0.107 0.91515
## haplogroupL2a 2.75000 1.14193 2.408 0.01794 *
## haplogroupL3b 1.75000 1.14193 1.532 0.12869
## haplogroupL3d 1.00000 0.88453 1.131 0.26107
## haplogroupL3e 2.25000 0.88453 2.544 0.01256 *
## haplogroupM5a 3.75000 1.14193 3.284 0.00143 **
## haplogroupM71a 1.75000 1.14193 1.532 0.12869
## haplogroupM7b 2.75000 1.14193 2.408 0.01794 *
## haplogroupN1b -0.25000 1.14193 -0.219 0.82717
## haplogroupR5a 2.75000 1.14193 2.408 0.01794 *
## haplogroupT1 3.75000 1.14193 3.284 0.00143 **
## haplogroupT1a 1.83333 0.65929 2.781 0.00653 **
## haplogroupT2b 0.16667 0.65929 0.253 0.80097
## haplogroupT2d -0.25000 1.14193 -0.219 0.82717
## haplogroupT2f -0.25000 0.88453 -0.283 0.77807
## haplogroupU2e 0.75000 1.14193 0.657 0.51289
## haplogroupU3a 1.75000 1.14193 1.532 0.12869
## haplogroupU4b -0.25000 1.14193 -0.219 0.82717
## haplogroupU5a 0.96429 0.64018 1.506 0.13528
## haplogroupU5b 1.75000 0.72222 2.423 0.01726 *
## haplogroupU6a 1.25000 0.88453 1.413 0.16084
## haplogroupV 0.91667 0.78009 1.175 0.24287
## haplogroupW 1.25000 1.14193 1.095 0.27641
## haplogroupX2c 2.75000 1.14193 2.408 0.01794 *
## haplogroupX2e 2.75000 1.14193 2.408 0.01794 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.021 on 96 degrees of freedom
## (1 observation deleted due to missingness)
## Multiple R-squared: 0.6024, Adjusted R-squared: 0.2379
## F-statistic: 1.653 on 88 and 96 DF, p-value: 0.008189All-by-all haplogroups kruskal-wallis
##
## Kruskal-Wallis rank sum test
##
## data: lvsd by haplogroup
## Kruskal-Wallis chi-squared = 106.96, df = 88, p-value = 0.0827LVSD vs superpopulation and autosomal population
Autosomal background on x-facet, mitochondrial superpopulation on the y-facet. LVSD on the y-axis, SNP-chip PCA component 1 on the x-axis.
Mitochondrial superpopulation on the x-facet, LVSD on the y-facet. PCA’s on the axes.
Micro haplogroup
Individual variants on LVSD
Potentially deleterious mutations in cohort
Subjects with potentially deleterious mutations with Genbank frequency <= 1% are below.
| patientphenotype | cnt | allele | gb_perc | subjects | meanlvsd |
|---|---|---|---|---|---|
| ADPD / Possibly LVNC-cardiomyopathy associated | 1 | A3397G | 0.3 | 833333 | 0.000000 |
| Adult-Onset Dystonia | 1 | A3796G | 0.54 | 835021 | 1.000000 |
| BD-associated | 1 | C114T | 0.45 | 823157 | 0.000000 |
| Cardiomyopathy | 1 | G3337A | 0.16 | 833306 | 1.000000 |
| CPEO | 1 | T12311C | 0.11 | 813584 | 1.500000 |
| Cyclic Vomiting Syndrome with Migraine | 1 | C16176T | 0.71 | 833333 | 0.000000 |
| DEAF | 1 | T1005C | 0.38 | 824932 | 0.000000 |
| DEAF enhancer | 1 | T5655C | 0.86 | 834220 | 3.000000 |
| DEAF, possibly LVNC-associated | 3 | T961C | 0.99 | 825058, 826309, 845419 | 1.333333 |
| Hypertensive end-stage renal disease | 1 | A10086G | 0.55 | 838492 | 2.000000 |
| LHON | 7 | A8836G, C3497T, G15812A, T14325C, G3736A, A4381G | 0.28, 0.36, 0.66, 0.1, 0.18, 0.01 | 819620, 824821, 828405, 843680, 845137… | 1.142857 |
| LHON / LDYT / DEAF / hypertension helper mut. | 1 | G11696A | 0.51 | 817016 | 3.000000 |
| LHON / SNHL / DEAF | 1 | G7444A | 0.37 | 816146 | 0.000000 |
| LHON modulator | 1 | A15951G | 0.96 | 841810 | 2.000000 |
| LHON-like, LHON, MELAS | 1 | A13528G | 0.1 | 830998 | 0.000000 |
| LHON; PD | 2 | T11253C | 0.62 | 827360, 833788 | 2.000000 |
| MELAS / DEAF enhancer / hypertension / LVNC | 1 | T3308C | 0.95 | 834220 | 3.000000 |
| Poss. hypertension factor | 1 | G3277A | 0.06 | 823334 | 2.000000 |
| possible HCM susceptibility | 4 | T12477C, G13135A | 0.66, 0.87 | 817189, 823148, 823884, 830097 | 2.000000 |
| Possibly DEAF-associated | 4 | T961G | 0.38 | 825415, 825906, 829530, 838893 | 2.000000 |
| Possibly LVNC-associated | 3 | T921C, A2755G | 0.69, 0.57 | 813584, 826552, 833306 | 1.166667 |
| Prostate Cancer | 4 | A7158G, T7080C, C5911T | 0.07, 0.1, 0.46 | 813584, 814994, 839722, 845419 | 1.125000 |
| Prostate Cancer / enriched in POAG cohort | 1 | G6480A | 0.38 | 825205 | 1.000000 |
| Prostate Cancer / hypertension | 2 | G5913A | 0.75 | 819620, 839771 | 1.000000 |
| Varied familial presentation / spastic paraparesis | 1 | G4284A | 0.01 | 845137 | 1.000000 |
| DEAF helper mut. | 1 | T10454C | 0.37 | 821863 | 0.000000 |
| DMDF+HCM / GDM / possibly LVNC cardiomyopathy-associated | 1 | T3398C | 0.36 | 828754 | 0.000000 |
| Myopathy | 1 | T5567C | 0.09 | 823919 | 0.000000 |
| Possible LHON factor | 2 | T12811C, A13637G | 0.91, 0.9 | 819758, 820935 | 3.000000 |
| Susceptibility to bullous pemphigoid | 1 | G8519A | 0.26 | 828793 | 1.000000 |
| Therapy-Resistant Epilepsy | 1 | C6489A | 0.21 | 826789 | 0.000000 |
| Thyroid Cancer Cell Line | 1 | A12634G | 0.28 | 826552 | 1.000000 |
High LVSD variants
The following variants are found in at least 2 high (>=2.0) LVSD subjects but never in very low (<1.0) subjects
| tpos | cnt | gb_avg | allele | locus | effect | haps | hap_percs | subjects |
|---|---|---|---|---|---|---|---|---|
| 225 | 2 | 0.77 | G225A | HVS2/OH/CSB1/ATT/D-Loop | non-coding | X2e, X2c | 20.69, 95.71 | 822335, 843690 |
| 239 | 3 | 1.31 | T239C | HVS2/OH/TFX/ATT/D-Loop | non-coding | T1, H6a, H6a | 0, 96.59, 96.59 | 823081, 827360, 833788 |
| 2387 | 2 | 0.24 | T2387C | 16S | rRNA | J1c, J1c | 3.92, 3.92 | 822754, 841525 |
| 3915 | 2 | 1.30 | G3915A | ND1 | syn:G=>G | H6a, H6a | 99.62, 99.62 | 827360, 833788 |
| 4164 | 2 | 1.04 | A4164G | ND1 | syn:M=>M | M7b, H5a | 97.64, 0.32 | 819758, 843976 |
| 4727 | 2 | 0.80 | A4727G | ND2 | syn:M=>M | H6a, H6a | 95.83, 95.83 | 827360, 833788 |
| 5198 | 2 | 0.28 | A5198G | ND2 | syn:L=>L | J1c, J1c | 10.37, 10.37 | 822754, 841525 |
| 5773 | 2 | 1.10 | G5773A | C/OL | tRNA | L3b, C1c | 100, 7.02 | 838492, 840544 |
| 6216 | 3 | 0.56 | T6216C | COI | syn:L=>L | U3a, C, B4b | 0, 0, 68.57 | 826190, 829368, 829844 |
| 6253 | 2 | 1.11 | T6253C | COI | non-syn:M=>T | C1c, H15a | 0, 100 | 828232, 841130 |
| 6371 | 2 | 1.06 | C6371T | COI | syn:S=>S | X2e, X2c | 100, 98.57 | 822335, 843690 |
| 6620 | 2 | 1.08 | T6620C | COI | syn:G=>G | K1b, J1b | 0, 0 | 839771, 843613 |
| 7768 | 2 | 1.85 | A7768G | COII | syn:M=>M | U5b, U5b | 99.49, 99.49 | 820935, 832692 |
| 8718 | 2 | 0.13 | A8718G | ATPase6 | syn:K=>K | M71a, X2e | 100, 0 | 817517, 822335 |
| 9380 | 2 | 1.10 | G9380A | COIII | syn:W=>W | H6a, H6a | 98.86, 98.86 | 827360, 833788 |
| 9899 | 5 | 1.06 | T9899C | COIII | syn:H=>H | T1a, T1, T1a, T1a, T1a | 69.25, 14.29, 69.25, 69.25, 69.25 | 822682, 823081, 825611, 830311, 836578 |
| 10192 | 2 | 0.19 | C10192T | ND3 | non-syn:S=>F | J1c, J1c | 3.8, 3.8 | 822754, 841525 |
| 10819 | 2 | 2.10 | A10819G | ND4 | syn:K=>K | L3e, L3e | 99.03, 99.03 | 823334, 835638 |
| 11002 | 2 | 0.95 | A11002G | ND4 | syn:Q=>Q | L3b, X2c | 81.41, 0 | 838492, 843690 |
| 11253 | 2 | 0.62 | T11253C | ND4 | non-syn:I=>T | H6a, H6a | 52.65, 52.65 | 827360, 833788 |
| 12633 | 5 | 1.21 | C12633A | ND5 | syn:S=>S | T1a, T1, T1a, T1a, T1a | 99.72, 100, 99.72, 99.72, 99.72 | 822682, 823081, 825611, 830311, 836578 |
| 13635 | 2 | 0.26 | T13635C | ND5 | syn:G=>G | C1b, R5a | 5.88, 78.72 | 818376, 837392 |
| 13879 | 2 | 0.78 | T13879C | ND5 | non-syn:S=>P | J1b, J1b | 63.98, 63.98 | 823389, 843613 |
| 13966 | 2 | 1.40 | A13966G | ND5 | non-syn:T=>A | X2e, X2c | 100, 100 | 822335, 843690 |
| 14040 | 2 | 0.52 | G14040A | ND5 | syn:Q=>Q | R5a, L3b | 74.47, 0 | 837392, 838492 |
| 14470 | 2 | 1.66 | T14470C | ND6 | syn:G=>G | X2e, X2c | 100, 100 | 822335, 843690 |
| 15758 | 2 | 0.88 | A15758G | Cytb | non-syn:I=>V | I2, H1a | 100, 1.93 | 826990, 843449 |
| 15784 | 2 | 3.29 | T15784C | Cytb | syn:P=>P | U5b, L2a | 0, 89.68 | 832692, 844845 |
| 15930 | 3 | 2.55 | G15930A | T/ATT | tRNA | C, C1c, C1c | 17.22, 100, 100 | 822655, 828232, 840544 |
| 16051 | 2 | 2.59 | A16051G | ATT/D-Loop/HVS1 | non-coding | K2b, C | 1.47, 19.87 | 823148, 829368 |
| 16186 | 2 | 1.24 | C16186T | ATT/D-Loop/HVS1/7S DNA | non-coding | T1a, T1a | 95.57, 95.57 | 830311, 836578 |
| 16192 | 4 | 4.27 | C16192T | ATT/D-Loop/HVS1/7S DNA | non-coding | U5a, H6a, A2a, J1b | 57.1, 1.14, 37.89, 5.93 | 825058, 827360, 833572, 843613 |
| 16218 | 2 | 0.62 | C16218T | ATT/D-Loop/HVS1/7S DNA | non-coding | HV, L0a | 0, 0.27 | 816255, 845419 |
| 16239 | 2 | 0.56 | C16239T, C16239G | ATT/D-Loop/HVS1/7S DNA | non-coding | H1, H3a | 7.34, 15.7 | 825090, 830330 |
| 16256 | 2 | 3.60 | C16256T | ATT/D-Loop/HVS1/7S DNA | non-coding | U5a, H3a | 94.01, 9.09 | 825058, 830330 |
| 16270 | 6 | 5.28 | C16270T | ATT/D-Loop/HVS1/7S DNA | non-coding | H1b, U5b, K2b, U5a, U5b, L1b | 7.01, 85.14, 45.59, 93.04, 85.14, 90.64 | 816856, 820935, 823148, 825058, 832692, 834220 |
| 16482 | 2 | 0.77 | A16482G | ATT/D-Loop/7S DNA | non-coding | H6a, H6a | 79.55, 79.55 | 827360, 833788 |
The following variants are found in at least 2 very low (<1.0) LVSD subjects but never in high (>=2.0) subjects
| tpos | cnt | gb_avg | allele | locus | effect | haps | hap_percs | subjects |
|---|---|---|---|---|---|---|---|---|
| 64 | 5 | 2.9600000 | C64T | HVS2/ATT/D-Loop/7S DNA | non-coding | A2, A2d, L0a, A2a, A2k | 75.42, 58.33, 54.62, 42.86, 80 | 823919, 824388, 825390, 827091, 837615 |
| 143 | 2 | 2.1900000 | G143A | HVS2/OH/ATT/D-Loop/7S DNA | non-coding | A2, C1b | 4.47, 4.58 | 823919, 828014 |
| 151 | 2 | 3.1800000 | C151T | HVS2/OH/ATT/D-Loop/7S DNA | non-coding | L1c, L1c | 72.59, 72.59 | 820786, 846683 |
| 228 | 2 | 2.7300000 | G228A | HVS2/OH/CSB1/ATT/D-Loop | non-coding | J1c, J1c | 79.15, 79.15 | 817189, 821863 |
| 236 | 2 | 1.3800000 | T236C | HVS2/OH/TFX/ATT/D-Loop | non-coding | L0a, L0a | 93.48, 93.48 | 825390, 839722 |
| 249 | 2 | 0.0850000 | A249T, A249G | HVS2/OH/TFX/ATT/D-Loop | non-coding | C1b, H5b | 0, 1.85 | 828014, 841150 |
| 316 | 2 | 1.6300000 | G316A | HVS2/OH/ATT/D-Loop | non-coding | L1c, L1c | 95.18, 95.18 | 820786, 846683 |
| 497 | 2 | 2.5800000 | C497T | ATT/D-Loop | non-coding | K1a, K1a | 96.93, 96.93 | 823157, 840957 |
| 930 | 4 | 2.0400000 | G930A | 12S | rRNA | T2b, T2b, T2b, T2b | 99.24, 99.24, 99.24, 99.24 | 821395, 821837, 828754, 832668 |
| 1048 | 2 | 3.6900000 | C1048T | 12S | rRNA | L0a, L0a | 100, 100 | 825390, 839722 |
| 1692 | 2 | 0.2700000 | A1692T, A1692G | 16S | rRNA | U6a, U4b | 21.1, 0 | 817443, 830998 |
| 2245 | 2 | 1.1100000 | A2245G | 16S | rRNA | L0a, L0a | 89.67, 89.67 | 825390, 839722 |
| 3516 | 2 | 3.2700000 | C3516A | ND1 | syn:L=>L | L0a, L0a | 99.73, 99.73 | 825390, 839722 |
| 4312 | 2 | 3.2800000 | C4312T | I | tRNA | L0a, L0a | 99.73, 99.73 | 825390, 839722 |
| 4561 | 2 | 0.7800000 | T4561C | ND2 | non-syn:V=>A | K2a, K2a | 100, 100 | 816468, 844801 |
| 4586 | 2 | 1.5800000 | T4586C | ND2 | syn:A=>A | L0a, L0a | 100, 100 | 825390, 839722 |
| 5147 | 5 | 4.1200000 | G5147A | ND2 | syn:T=>T | T2b, T2b, L0a, T2b, T2b | 99.62, 99.62, 50, 99.62, 99.62 | 821395, 821837, 825390, 828754, 832668 |
| 5426 | 2 | 1.0500000 | T5426C | ND2 | syn:H=>H | T2b, T2f | 1.14, 94.83 | 821837, 826789 |
| 5442 | 2 | 4.4300000 | T5442C | ND2 | non-syn:F=>L | L0a, L0a | 99.73, 99.73 | 825390, 839722 |
| 5471 | 3 | 1.0600000 | G5471A | ND2 | syn:T=>T | U6a, N1b, H5b | 22.48, 98.86, 100 | 817443, 819620, 841150 |
| 5603 | 2 | 1.2900000 | C5603T | A | tRNA | L0a, L0a | 97.83, 97.83 | 825390, 839722 |
| 5951 | 2 | 1.4600000 | A5951G | COI | syn:G=>G | L1c, L1c | 99.34, 99.34 | 820786, 846683 |
| 6071 | 2 | 1.4700000 | T6071C | COI | syn:V=>V | L1c, L1c | 99.56, 99.56 | 820786, 846683 |
| 6185 | 2 | 3.3600000 | T6185C | COI | syn:F=>F | L0a, L0a | 100, 100 | 825390, 839722 |
| 6917 | 2 | 0.3600000 | G6917A | COI | syn:V=>V | L1c, L1c | 18.42, 18.42 | 820786, 846683 |
| 7389 | 3 | 2.4200000 | T7389C | COI | non-syn:Y=>H | L1c, A2, L1c | 99.78, 2.23, 99.78 | 820786, 825934, 846683 |
| 7930 | 2 | 0.1300000 | A7930T | COII | syn:G=>G | H31, H31 | 96.43, 96.43 | 836223, 838511 |
| 8251 | 3 | 6.4400000 | G8251A | COII | syn:G=>G | N1b, L1c, I1 | 96.59, 17.32, 100 | 819620, 820786, 826457 |
| 8428 | 2 | 1.1600000 | C8428T | ATPase8 | syn:F=>F | L0a, L0a | 100, 100 | 825390, 839722 |
| 8460 | 2 | 0.6400000 | A8460G | ATPase8 | non-syn:N=>S | L0a, A2k | 48.91, 60 | 825390, 837615 |
| 8566 | 2 | 1.2300000 | A8566G | ATPase8/ATPase6 | syn:Q=>Q | L0a, L0a | 100, 100 | 825390, 839722 |
| 8602 | 2 | 0.1600000 | T8602C | ATPase6 | non-syn:F=>L | H1g, H1g | 97.3, 97.3 | 826167, 829029 |
| 9042 | 2 | 3.2900000 | C9042T | ATPase6 | syn:H=>H | L0a, L0a | 100, 100 | 825390, 839722 |
| 9055 | 3 | 4.9300000 | G9055A | ATPase6 | non-syn:A=>T | K1a, K1a, K2a | 99.17, 99.17, 100 | 823157, 840957, 844801 |
| 9072 | 2 | 1.4300000 | A9072G | ATPase6 | syn:S=>S | L1c, L1c | 99.56, 99.56 | 820786, 846683 |
| 9347 | 2 | 3.2500000 | A9347G | COIII | syn:L=>L | L0a, L0a | 100, 100 | 825390, 839722 |
| 9716 | 2 | 1.0300000 | T9716C | COIII | syn:G=>G | K2a, K2a | 100, 100 | 816468, 844801 |
| 9755 | 3 | 3.1300000 | G9755A | COIII | syn:E=>E | J1c, L0a, L0a | 1.73, 100, 100 | 821908, 825390, 839722 |
| 9818 | 2 | 1.5700000 | C9818T | COIII | syn:H=>H | L0a, L0a | 100, 100 | 825390, 839722 |
| 9966 | 2 | 0.6900000 | G9966A | COIII | non-syn:V=>I | I1, L1c | 96.67, 8.77 | 826457, 846683 |
| 10238 | 2 | 6.2600000 | T10238C | ND3 | syn:I=>I | N1b, I1 | 98.86, 100 | 819620, 826457 |
| 10586 | 2 | 1.8700000 | G10586A | ND4L | syn:S=>S | L1c, L1c | 99.56, 99.56 | 820786, 846683 |
| 10664 | 2 | 3.2800000 | C10664T | ND4L | syn:V=>V | L0a, L0a | 100, 100 | 825390, 839722 |
| 10771 | 2 | 0.1400000 | A10771G | ND4 | syn:L=>L | H31, H31 | 92.86, 92.86 | 836223, 838511 |
| 10915 | 2 | 3.9900000 | T10915C | ND4 | syn:C=>C | L0a, L0a | 99.18, 99.18 | 825390, 839722 |
| 11176 | 2 | 1.4500000 | G11176A | ND4 | syn:Q=>Q | L0a, L0a | 100, 100 | 825390, 839722 |
| 11302 | 2 | 0.2700000 | C11302T | ND4 | syn:L=>L | L1c, L1c | 18.42, 18.42 | 820786, 846683 |
| 11314 | 2 | 0.2000000 | A11314G | ND4 | syn:E=>E | L1c, A2d | 0, 45.83 | 820786, 824388 |
| 11641 | 2 | 1.2900000 | A11641G | ND4 | syn:M=>M | L0a, L0a | 100, 100 | 825390, 839722 |
| 11812 | 7 | 3.3000000 | A11812G | ND4 | syn:L=>L | T2f, T2b, T2b, T2d, T2f, T2b, T2b | 100, 99.43, 99.43, 100, 100, 99.43, 99.43 | 818356, 821395, 821837, 821949, 826789, 828754, 832668 |
| 12720 | 2 | 3.0500000 | A12720G | ND5 | syn:M=>M | L0a, L0a | 99.46, 99.46 | 825390, 839722 |
| 12810 | 2 | 2.2900000 | A12810G | ND5 | syn:W=>W | L1c, L1c | 99.56, 99.56 | 820786, 846683 |
| 13276 | 2 | 3.2400000 | A13276G | ND5 | non-syn:M=>V | L0a, L0a | 99.18, 99.18 | 825390, 839722 |
| 13485 | 2 | 1.4200000 | A13485G | ND5 | syn:M=>M | L1c, L1c | 98.68, 98.68 | 820786, 846683 |
| 13789 | 2 | 2.2700000 | T13789C | ND5 | non-syn:Y=>H | L1c, L1c | 99.78, 99.78 | 820786, 846683 |
| 13934 | 5 | 1.1900000 | C13934T | ND5 | non-syn:T=>M | J1c, D1, J1c, J1c, J1c | 19.93, 0.94, 19.93, 19.93, 19.93 | 817189, 817866, 821640, 821863, 821908 |
| 14000 | 2 | 1.4600000 | T14000A | ND5 | non-syn:L=>Q | L1c, L1c | 99.78, 99.78 | 820786, 846683 |
| 14106 | 2 | 0.0800000 | T14106C | ND5 | syn:S=>S | A2, L0a | 0.56, 4.89 | 823919, 839722 |
| 14178 | 3 | 2.7700000 | T14178C | ND6 | non-syn:I=>V | L1c, H27a, L1c | 99.78, 0, 99.78 | 820786, 831554, 846683 |
| 14233 | 7 | 3.6600000 | A14233G | ND6 | syn:D=>D | T2f, T2b, T2b, T2d, T2f, T2b, T2b | 98.28, 99.24, 99.24, 100, 98.28, 99.24, 99.24 | 818356, 821395, 821837, 821949, 826789, 828754, 832668 |
| 14305 | 2 | 0.5600000 | G14305A | ND6 | syn:S=>S | K2a, K2a | 23.24, 23.24 | 816468, 844801 |
| 14308 | 2 | 1.7400000 | T14308C | ND6 | syn:G=>G | L0a, L0a | 97.28, 97.28 | 825390, 839722 |
| 14560 | 2 | 2.7900000 | G14560A | ND6 | syn:V=>V | L1c, L1c | 99.34, 99.34 | 820786, 846683 |
| 14911 | 2 | 1.4300000 | C14911T | Cytb | syn:Y=>Y | L1c, L1c | 98.68, 98.68 | 820786, 846683 |
| 15136 | 2 | 1.2200000 | C15136T | Cytb | syn:G=>G | L0a, L0a | 100, 100 | 825390, 839722 |
| 15226 | 2 | 0.3300000 | A15226G | Cytb | syn:L=>L | L1c, L1c | 17.98, 17.98 | 820786, 846683 |
| 15431 | 2 | 1.5900000 | G15431A | Cytb | non-syn:A=>T | L0a, L0a | 99.73, 99.73 | 825390, 839722 |
| 15905 | 2 | 0.3900000 | T15905C | T | tRNA | L1c, L1c | 17.98, 17.98 | 820786, 846683 |
| 15924 | 4 | 4.0200000 | A15924G | T | tRNA | N1b, K1a, I1, A2k | 1.14, 14.64, 93.33, 80 | 819620, 823157, 826457, 837615 |
| 15978 | 2 | 0.3000000 | C15978T | P/ATT | tRNA | L1c, L1c | 18.42, 18.42 | 820786, 846683 |
| 16176 | 2 | 0.4600000 | C16176G, C16176T | ATT/D-Loop/HVS1/7S DNA | non-coding | N1b, H82 | 73.86, 0 | 819620, 833333 |
| 16179 | 2 | 0.7200000 | C16179T | ATT/D-Loop/HVS1/7S DNA | non-coding | K1c, B2 | 0, 0.67 | 815368, 816146 |
| 16188 | 2 | 0.9800000 | C16188G | ATT/D-Loop/HVS1/7S DNA | non-coding | L0a, L0a | 82.88, 82.88 | 825390, 839722 |
| 16209 | 2 | 2.7200000 | T16209C | ATT/D-Loop/HVS1/7S DNA | non-coding | L1c, H1a | 5.26, 15.09 | 820786, 833669 |
| 16215 | 2 | 0.2500000 | A16215G | ATT/D-Loop/HVS1/7S DNA | non-coding | H1e, L1c | 0.51, 7.46 | 823637, 846683 |
| 16220 | 2 | 0.1950000 | A16220C, A16220G | ATT/D-Loop/HVS1/7S DNA | non-coding | H1b, H82 | 2.74, 100 | 826379, 833333 |
| 16222 | 2 | 0.8100000 | C16222T | ATT/D-Loop/HVS1/7S DNA | non-coding | J1b, J1b | 73.73, 73.73 | 819501, 836933 |
| 16224 | 4 | 5.0000000 | T16224C | ATT/D-Loop/HVS1/7S DNA | non-coding | T2b, K1a, K1a, K2a | 0.38, 95.4, 95.4, 95.14 | 821395, 823157, 840957, 844801 |
| 16230 | 2 | 3.1600000 | A16230G | ATT/D-Loop/HVS1/7S DNA | non-coding | L0a, L0a | 94.02, 94.02 | 825390, 839722 |
| 16261 | 2 | 7.4700000 | C16261T | ATT/D-Loop/HVS1/7S DNA | non-coding | J1b, H7a | 95.76, 83.33 | 836933, 841268 |
| 16316 | 3 | 0.2933333 | A16316T, A16316G | ATT/D-Loop/HVS1/7S DNA | non-coding | A2a, A2a, H27a | 0, 0, 100 | 817954, 827091, 831554 |
| 16317 | 3 | 0.0000000 | A16317C | ATT/D-Loop/HVS1/7S DNA | non-coding | C1b, A2a, C1b | 0, 0, 0 | 824932, 827091, 828014 |
mtGWAS
GLM using both haplogroup and non-haplogroup defining variants
p.value < 0.05 before correction for multiple testing
| tpos | hapsnp_p.val | tnt | qnt | calc_locus | gb_perc | allele | haps | hap_percs | subjects | mean_lvsd |
|---|---|---|---|---|---|---|---|---|---|---|
| 225 | 0.0238794 | G | A | HVS2/OH/CSB1/ATT/D-Loop | 0.77 | G225A | X2e | 20.69 | 822335 | 3.000 |
| 239 | 0.0243111 | T | C | HVS2/OH/TFX/ATT/D-Loop | 1.31 | T239C | T1 | 0 | 823081 | 4.000 |
| 437 | 0.0411979 | C | T | OH/PL/TFL/ATT/D-Loop | 0.07 | C437T | A2a | 1.86 | 823650 | 3.000 |
| 487 | 0.0411979 | A | G | ATT/D-Loop | 0.02 | A487G | A2a | 2.48 | 823650 | 3.000 |
| 2387 | 0.0324802 | T | C | 16S | 0.24 | T2387C | J1c, J1c | 3.92, 3.92 | 822754, 841525 | 2.500 |
| 3565 | 0.0411979 | A | G | ND1 | 0.10 | A3565G | A2a | 2.48 | 823650 | 3.000 |
| 5046 | 0.0423120 | G | A | ND2 | 2.15 | G5046A | W | 0 | 834209 | 1.500 |
| 5102 | 0.0140978 | A | G | ND2 | 0.01 | A5102G | H11a | 0 | 825906 | 4.000 |
| 5147 | 0.0203247 | G | A | ND2 | 4.12 | G5147A | L0a, L0a | 50, 50 | 825390, 845137 | 0.500 |
| 5198 | 0.0324802 | A | G | ND2 | 0.28 | A5198G | J1c, J1c | 10.37, 10.37 | 822754, 841525 | 2.500 |
| 5252 | 0.0140978 | G | A | ND2 | 0.34 | G5252A | H11a | 0 | 825906 | 4.000 |
| 5461 | 0.0377832 | C | T | ND2 | 0.03 | C5461T | K2b | 0 | 823148 | 3.000 |
| 5985 | 0.0103637 | G | A | COI | 0.11 | G5985A | T1 | 0 | 823081 | 4.000 |
| 6446 | 0.0423120 | G | A | COI | 0.69 | G6446A | L1b | 2.25 | 834220 | 3.000 |
| 7307 | 0.0411979 | A | G | COI | 0.02 | A7307G | A2a | 1.86 | 823650 | 3.000 |
| 9458 | 0.0423120 | C | T | COIII | 0.17 | C9458T | L1b | 1.12 | 834220 | 3.000 |
| 9899 | 0.0002890 | T | C | COIII | 1.06 | T9899C | T1a, T1, T1a, T1a, T1a, T1a | 69.25, 14.29, 69.25, 69.25, 69.25, 69.25 | 822682, 823081, 825121, 825611, 830311, 836578 | 2.500 |
| 10192 | 0.0324802 | C | T | ND3 | 0.19 | C10192T | J1c, J1c | 3.8, 3.8 | 822754, 841525 | 2.500 |
| 11812 | 0.0058209 | A | G | ND4 | 3.30 | A11812G | C1b | 1.96 | 846183 | 3.000 |
| 14587 | 0.0140978 | A | G | ND6 | 0.53 | A14587G | H11a | 28.8 | 825906 | 4.000 |
| 15236 | 0.0411979 | A | G | Cytb | 1.10 | A15236G | A2a | 0 | 823650 | 3.000 |
| 15412 | 0.0411979 | T | C | Cytb | 0.11 | T15412C | A2a | 0 | 823650 | 3.000 |
| 16092 | 0.0140978 | T | C | ATT/D-Loop/HVS1 | 1.47 | T16092C | H11a | 24 | 825906 | 4.000 |
| 16163 | 0.0032930 | A | G | ATT/D-Loop/HVS1/7S DNA/TAS | 1.40 | A16163G | L1c, T1 | 8.55, 57.14 | 820786, 823081 | 2.000 |
| 16239 | 0.0039954 | C | G | ATT/D-Loop/HVS1/7S DNA | 0.06 | C16239G | H3a | 15.7 | 830330 | 4.000 |
| 16239 | 0.0039954 | C | T | ATT/D-Loop/HVS1/7S DNA | 1.06 | C16239T | H1 | 7.34 | 825090 | 3.000 |
| 16254 | 0.0140978 | A | G | ATT/D-Loop/HVS1/7S DNA | 0.13 | A16254G | H11a | 0 | 825906 | 4.000 |
| 16270 | 0.0101111 | C | T | ATT/D-Loop/HVS1/7S DNA | 5.28 | C16270T | H1b, K2b, H1b, K2b | 7.01, 45.59, 7.01, 45.59 | 816856, 823148, 827951, 830097 | 1.875 |
| 16293 | 0.0247849 | A | G | ATT/D-Loop/HVS1/7S DNA | 2.28 | A16293G | L0a, L0a | 27.17, 27.17 | 839722, 845419 | 1.000 |
| 16317 | 0.0217274 | A | C | ATT/D-Loop/HVS1/7S DNA | 0.00 | A16317C | C1b, A2a, C1b | 0, 0, 0 | 824932, 827091, 828014 | 0.000 |
GLM - non-haplogroup defining variants only
p.value < 0.05 before correction for multiple testing
| tpos | snponly_p.val | qnt | tnt | calc_locus | gb_perc | allele | haps | hap_percs | subjects | mean_lvsd |
|---|---|---|---|---|---|---|---|---|---|---|
| 151 | 0.0449163 | T | C | HVS2/OH/ATT/D-Loop/7S DNA | 3.18 | C151T | L1c, L1c | 72.59, 72.59 | 820786, 846683 | 0.000 |
| 154 | 0.0339510 | C | T | HVS2/OH/ATT/D-Loop/7S DNA | 0.07 | T154C | M5a | 0.85 | 823884 | 4.000 |
| 225 | 0.0220812 | A | G | HVS2/OH/CSB1/ATT/D-Loop | 0.77 | G225A | X2e | 20.69 | 822335 | 3.000 |
| 239 | 0.0291555 | C | T | HVS2/OH/TFX/ATT/D-Loop | 1.31 | T239C | T1 | 0 | 823081 | 4.000 |
| 5102 | 0.0127407 | G | A | ND2 | 0.01 | A5102G | H11a | 0 | 825906 | 4.000 |
| 5147 | 0.0445695 | A | G | ND2 | 4.12 | G5147A | L0a, L0a | 50, 50 | 825390, 845137 | 0.500 |
| 5252 | 0.0127407 | A | G | ND2 | 0.34 | G5252A | H11a | 0 | 825906 | 4.000 |
| 5985 | 0.0139742 | A | G | COI | 0.11 | G5985A | T1 | 0 | 823081 | 4.000 |
| 6917 | 0.0449163 | A | G | COI | 0.36 | G6917A | L1c, L1c | 18.42, 18.42 | 820786, 846683 | 0.000 |
| 9899 | 0.0031598 | C | T | COIII | 1.06 | T9899C | T1a, T1, T1a, T1a, T1a, T1a | 69.25, 14.29, 69.25, 69.25, 69.25, 69.25 | 822682, 823081, 825121, 825611, 830311, 836578 | 2.500 |
| 11302 | 0.0449163 | T | C | ND4 | 0.27 | C11302T | L1c, L1c | 18.42, 18.42 | 820786, 846683 | 0.000 |
| 12681 | 0.0339510 | C | T | ND5 | 0.20 | T12681C | M5a | 1.69 | 823884 | 4.000 |
| 13105 | 0.0418467 | G | A | ND5 | 7.77 | A13105G | D1d | 40 | 823260 | 1.000 |
| 14587 | 0.0127407 | G | A | ND6 | 0.53 | A14587G | H11a | 28.8 | 825906 | 4.000 |
| 15226 | 0.0449163 | G | A | Cytb | 0.33 | A15226G | L1c, L1c | 17.98, 17.98 | 820786, 846683 | 0.000 |
| 15301 | 0.0376168 | A | G | Cytb | 27.55 | G15301A | B4c | 40.74 | 824821 | 1.000 |
| 15784 | 0.0416055 | C | T | Cytb | 3.29 | T15784C | U5b | 0 | 832692 | 3.000 |
| 15978 | 0.0449163 | T | C | P/ATT | 0.30 | C15978T | L1c, L1c | 18.42, 18.42 | 820786, 846683 | 0.000 |
| 16092 | 0.0127407 | C | T | ATT/D-Loop/HVS1 | 1.47 | T16092C | H11a | 24 | 825906 | 4.000 |
| 16163 | 0.0279064 | G | A | ATT/D-Loop/HVS1/7S DNA/TAS | 1.40 | A16163G | L1c, T1 | 8.55, 57.14 | 820786, 823081 | 2.000 |
| 16239 | 0.0033374 | G | C | ATT/D-Loop/HVS1/7S DNA | 0.06 | C16239G | H3a | 15.7 | 830330 | 4.000 |
| 16239 | 0.0033374 | T | C | ATT/D-Loop/HVS1/7S DNA | 1.06 | C16239T | H1 | 7.34 | 825090 | 3.000 |
| 16254 | 0.0127407 | G | A | ATT/D-Loop/HVS1/7S DNA | 0.13 | A16254G | H11a | 0 | 825906 | 4.000 |
| 16270 | 0.0188273 | T | C | ATT/D-Loop/HVS1/7S DNA | 5.28 | C16270T | H1b, K2b, H1b, K2b | 7.01, 45.59, 7.01, 45.59 | 816856, 823148, 827951, 830097 | 1.875 |
GLMs
Haplogroups of interest
H
Enrichment
Are there any differences in variants between the 10 >=3’s and the 21 0’s?
Enriched in high LVSD (>1fc)
| tpos | tnt | qnt | calc_locus | gb_perc | hot | cold | enrichment | allele |
|---|---|---|---|---|---|---|---|---|
| 55 | T | C | ATT/D-Loop/7S DNA | 0.20 | 1 | 0 | Inf | T55C |
| 57 | T | C | HVS2/ATT/D-Loop/7S DNA | 0.20 | 1 | 0 | Inf | T57C |
| 73 | A | G | HVS2/ATT/D-Loop/7S DNA | 73.71 | 1 | 1 | 1.070389 | A73G |
| 189 | A | C | HVS2/OH/ATT/D-Loop/7S DNA | 1.41 | 1 | 1 | 1.070389 | A189C |
| 189 | A | G | HVS2/OH/ATT/D-Loop/7S DNA | 5.51 | 1 | 1 | 1.070389 | A189G |
| 379 | A | G | OH/mt4H/ATT/D-Loop | 0.01 | 1 | 0 | Inf | A379G |
| 961 | T | C | 12S | 0.99 | 2 | 2 | 1.070389 | T961C |
| 961 | T | G | 12S | 0.38 | 2 | 2 | 1.070389 | T961G |
| 1187 | T | C | 12S | 0.08 | 1 | 0 | Inf | T1187C |
| 1822 | T | C | 16S | 0.57 | 1 | 0 | Inf | T1822C |
| 1842 | A | G | 16S | 0.33 | 1 | 0 | Inf | A1842G |
| 1926 | A | G | 16S | 0.03 | 1 | 0 | Inf | A1926G |
| 3333 | C | T | ND1 | 0.14 | 1 | 0 | Inf | C3333T |
| 3579 | A | G | ND1 | 0.05 | 1 | 0 | Inf | A3579G |
| 3666 | G | A | ND1 | 2.77 | 1 | 0 | Inf | G3666A |
| 5102 | A | G | ND2 | 0.01 | 1 | 0 | Inf | A5102G |
| 5252 | G | A | ND2 | 0.34 | 1 | 0 | Inf | G5252A |
| 6253 | T | C | COI | 1.11 | 1 | 0 | Inf | T6253C |
| 6365 | T | C | COI | 0.32 | 1 | 1 | 1.070389 | T6365C |
| 6629 | A | G | COI | 0.27 | 1 | 0 | Inf | A6629G |
| 6776 | T | C | COI | 1.94 | 2 | 2 | 1.070389 | T6776C |
| 7220 | T | C | COI | 0.07 | 1 | 0 | Inf | T7220C |
| 8448 | T | C | ATPase8 | 0.43 | 2 | 1 | 2.070389 | T8448C |
| 8540 | T | C | ATPase8/ATPase6 | 0.02 | 1 | 0 | Inf | T8540C |
| 8745 | A | G | ATPase6 | 0.02 | 1 | 0 | Inf | A8745G |
| 9181 | A | G | ATPase6 | 0.22 | 1 | 0 | Inf | A9181G |
| 10364 | G | A | ND3 | 0.07 | 1 | 0 | Inf | G10364A |
| 10653 | G | A | ND4L | 0.05 | 1 | 0 | Inf | G10653A |
| 11410 | T | C | ND4 | 0.16 | 1 | 0 | Inf | T11410C |
| 11914 | G | A | ND4 | 11.02 | 1 | 0 | Inf | G11914A |
| 13404 | T | C | ND5 | 0.18 | 1 | 0 | Inf | T13404C |
| 13708 | G | A | ND5 | 6.82 | 1 | 0 | Inf | G13708A |
| 13759 | G | A | ND5 | 2.93 | 2 | 1 | 2.070389 | G13759A |
| 14070 | A | G | ND5 | 0.34 | 1 | 0 | Inf | A14070G |
| 14587 | A | G | ND6 | 0.53 | 1 | 0 | Inf | A14587G |
| 14953 | C | T | Cytb | 0.12 | 1 | 0 | Inf | C14953T |
| 16092 | T | C | ATT/D-Loop/HVS1 | 1.47 | 1 | 0 | Inf | T16092C |
| 16140 | T | C | ATT/D-Loop/HVS1/7S DNA | 1.30 | 1 | 0 | Inf | T16140C |
| 16162 | A | G | ATT/D-Loop/HVS1/7S DNA/TAS | 1.43 | 1 | 1 | 1.070389 | A16162G |
| 16184 | C | T | ATT/D-Loop/HVS1/7S DNA | 0.72 | 1 | 0 | Inf | C16184T |
| 16209 | T | C | ATT/D-Loop/HVS1/7S DNA | 2.72 | 1 | 1 | 1.070389 | T16209C |
| 16239 | C | G | ATT/D-Loop/HVS1/7S DNA | 0.06 | 2 | 0 | Inf | C16239G |
| 16239 | C | T | ATT/D-Loop/HVS1/7S DNA | 1.06 | 2 | 0 | Inf | C16239T |
| 16254 | A | G | ATT/D-Loop/HVS1/7S DNA | 0.13 | 1 | 0 | Inf | A16254G |
| 16256 | C | T | ATT/D-Loop/HVS1/7S DNA | 3.60 | 1 | 0 | Inf | C16256T |
| 16293 | A | G | ATT/D-Loop/HVS1/7S DNA | 2.28 | 3 | 1 | 2.655352 | A16293G |
| 16311 | T | C | ATT/D-Loop/HVS1/7S DNA | 20.66 | 3 | 1 | 2.655352 | T16311C |
Enriched in low LVSD (<-1fc)
| tpos | tnt | qnt | calc_locus | gb_perc | hot | cold | enrichment | allele |
|---|---|---|---|---|---|---|---|---|
| 150 | C | T | HVS2/OH/ATT/D-Loop/7S DNA | 11.81 | 0 | 1 | -Inf | C150T |
| 152 | T | C | HVS2/OH/ATT/D-Loop/7S DNA | 25.84 | 1 | 6 | -1.514573 | T152C |
| 204 | T | C | HVS2/OH/ATT/D-Loop | 6.07 | 0 | 1 | -Inf | T204C |
| 242 | C | T | HVS2/OH/TFX/ATT/D-Loop | 0.39 | 0 | 1 | -Inf | C242T |
| 249 | A | G | HVS2/OH/TFX/ATT/D-Loop | 0.17 | 0 | 1 | -Inf | A249G |
| 249 | A | T | HVS2/OH/TFX/ATT/D-Loop | 0.00 | 0 | 1 | -Inf | A249T |
| 408 | T | A | OH/PL/ATT/D-Loop | 0.21 | 0 | 1 | -Inf | T408A |
| 575 | C | T | D-Loop | 0.11 | 0 | 1 | -Inf | C575T |
| 951 | G | A | 12S | 0.79 | 0 | 1 | -Inf | G951A |
| 1503 | G | A | 12S | 0.28 | 0 | 1 | -Inf | G1503A |
| 1719 | G | A | 16S | 5.07 | 0 | 1 | -Inf | G1719A |
| 2352 | T | C | 16S | 2.62 | 0 | 1 | -Inf | T2352C |
| 2581 | A | G | 16S | 0.29 | 0 | 1 | -Inf | A2581G |
| 2882 | T | C | 16S | 0.01 | 0 | 1 | -Inf | T2882C |
| 3197 | T | C | 16S | 4.21 | 0 | 1 | -Inf | T3197C |
| 3397 | A | G | ND1 | 0.30 | 0 | 1 | -Inf | A3397G |
| 3906 | T | C | ND1 | 0.03 | 0 | 1 | -Inf | T3906C |
| 4227 | A | G | ND1 | 0.10 | 0 | 1 | -Inf | A4227G |
| 4336 | T | C | Q | 1.04 | 0 | 2 | -Inf | T4336C |
| 4512 | G | A | ND2 | 0.06 | 0 | 1 | -Inf | G4512A |
| 4736 | T | C | ND2 | 0.17 | 0 | 1 | -Inf | T4736C |
| 4793 | A | G | ND2 | 0.85 | 0 | 1 | -Inf | A4793G |
| 5054 | G | C | ND2 | 0.07 | 0 | 1 | -Inf | G5054C |
| 5460 | G | A | ND2 | 6.25 | 0 | 1 | -Inf | G5460A |
| 5471 | G | A | ND2 | 1.06 | 0 | 1 | -Inf | G5471A |
| 5480 | A | G | ND2 | 0.18 | 0 | 1 | -Inf | A5480G |
| 6126 | A | G | COI | 0.01 | 0 | 1 | -Inf | A6126G |
| 7471 | C | T | S(UCN) | 0.05 | 0 | 1 | -Inf | C7471T |
| 7645 | T | C | COII | 0.28 | 0 | 1 | -Inf | T7645C |
| 7930 | A | T | COII | 0.13 | 0 | 2 | -Inf | A7930T |
| 8429 | C | T | ATPase8 | 0.04 | 0 | 1 | -Inf | C8429T |
| 8602 | T | C | ATPase6 | 0.16 | 0 | 2 | -Inf | T8602C |
| 9163 | G | A | ATPase6 | 0.06 | 0 | 1 | -Inf | G9163A |
| 9391 | C | T | COIII | 0.07 | 0 | 1 | -Inf | C9391T |
| 9489 | G | A | COIII | 0.02 | 0 | 1 | -Inf | G9489A |
| 9581 | T | C | COIII | 0.14 | 0 | 1 | -Inf | T9581C |
| 10217 | A | G | ND3 | 0.12 | 0 | 1 | -Inf | A10217G |
| 10493 | T | C | ND4L | 0.27 | 0 | 1 | -Inf | T10493C |
| 10771 | A | G | ND4 | 0.14 | 0 | 2 | -Inf | A10771G |
| 11101 | A | G | ND4 | 0.14 | 0 | 1 | -Inf | A11101G |
| 11719 | G | A | ND4 | 75.36 | 0 | 1 | -Inf | G11719A |
| 11864 | T | C | ND4 | 0.17 | 0 | 1 | -Inf | T11864C |
| 11969 | G | A | ND4 | 1.51 | 0 | 1 | -Inf | G11969A |
| 14097 | C | T | ND5 | 0.07 | 0 | 1 | -Inf | C14097T |
| 14178 | T | C | ND6 | 2.77 | 0 | 1 | -Inf | T14178C |
| 14212 | T | C | ND6 | 1.86 | 0 | 2 | -Inf | T14212C |
| 14325 | T | C | ND6 | 0.10 | 0 | 1 | -Inf | T14325C |
| 14359 | C | T | ND6 | 0.00 | 0 | 1 | -Inf | C14359T |
| 14401 | A | G | ND6 | 0.02 | 0 | 1 | -Inf | A14401G |
| 14497 | A | G | ND6 | 0.05 | 0 | 1 | -Inf | A14497G |
| 14857 | T | C | Cytb | 0.06 | 0 | 1 | -Inf | T14857C |
| 14861 | G | A | Cytb | 0.27 | 0 | 1 | -Inf | G14861A |
| 14871 | T | C | Cytb | 0.02 | 0 | 1 | -Inf | T14871C |
| 15430 | C | T | Cytb | 0.01 | 0 | 1 | -Inf | C15430T |
| 15511 | T | C | Cytb | 0.30 | 0 | 1 | -Inf | T15511C |
| 15646 | C | T | Cytb | 0.06 | 0 | 1 | -Inf | C15646T |
| 15817 | A | G | Cytb | 0.11 | 0 | 1 | -Inf | A15817G |
| 15833 | C | T | Cytb | 0.66 | 0 | 1 | -Inf | C15833T |
| 15992 | A | G | P/ATT | 0.01 | 0 | 1 | -Inf | A15992G |
| 16093 | T | C | ATT/D-Loop/HVS1 | 5.66 | 0 | 2 | -Inf | T16093C |
| 16126 | T | C | ATT/D-Loop/HVS1/7S DNA | 11.58 | 0 | 1 | -Inf | T16126C |
| 16129 | G | A | ATT/D-Loop/HVS1/7S DNA | 13.07 | 0 | 2 | -Inf | G16129A |
| 16129 | G | C | ATT/D-Loop/HVS1/7S DNA | 0.69 | 0 | 2 | -Inf | G16129C |
| 16176 | C | G | ATT/D-Loop/HVS1/7S DNA | 0.21 | 0 | 1 | -Inf | C16176G |
| 16176 | C | T | ATT/D-Loop/HVS1/7S DNA | 0.71 | 0 | 1 | -Inf | C16176T |
| 16215 | A | G | ATT/D-Loop/HVS1/7S DNA | 0.25 | 0 | 1 | -Inf | A16215G |
| 16220 | A | C | ATT/D-Loop/HVS1/7S DNA | 0.33 | 0 | 2 | -Inf | A16220C |
| 16220 | A | G | ATT/D-Loop/HVS1/7S DNA | 0.06 | 0 | 2 | -Inf | A16220G |
| 16261 | C | T | ATT/D-Loop/HVS1/7S DNA | 7.47 | 0 | 1 | -Inf | C16261T |
| 16316 | A | G | ATT/D-Loop/HVS1/7S DNA | 0.88 | 0 | 1 | -Inf | A16316G |
| 16316 | A | T | ATT/D-Loop/HVS1/7S DNA | 0.00 | 0 | 1 | -Inf | A16316T |
| 16357 | T | C | ATT/D-Loop/HVS1/7S DNA | 1.09 | 0 | 1 | -Inf | T16357C |
| 16390 | G | A | ATT/D-Loop/7S DNA | 5.82 | 0 | 1 | -Inf | G16390A |
Sex differences in H
H has differences in the number of high LVSD subjects by gender. There is no discernable interaction with any H subclades.
## # A tibble: 4 x 3
## sex `lvsd >= 3` cnt
## <fct> <lgl> <int>
## 1 1 FALSE 24
## 2 1 TRUE 2
## 3 2 FALSE 22
## 4 2 TRUE 8
T
Enrichment
Are there any differences in variants between the 3 >=3’s and the 7 0’s?
Enriched in high LVSD (>1fc)
| tpos | tnt | qnt | calc_locus | gb_perc | hot | cold | enrichment | allele |
|---|---|---|---|---|---|---|---|---|
| 152 | T | C | HVS2/OH/ATT/D-Loop/7S DNA | 25.84 | 3 | 2 | 1.807355 | T152C |
| 195 | T | C | HVS2/OH/ATT/D-Loop | 20.51 | 2 | 2 | 1.222392 | T195C |
| 239 | T | C | HVS2/OH/TFX/ATT/D-Loop | 1.31 | 1 | 0 | Inf | T239C |
| 469 | C | T | ATT/D-Loop | 0.04 | 1 | 0 | Inf | C469T |
| 5985 | G | A | COI | 0.11 | 1 | 0 | Inf | G5985A |
| 9899 | T | C | COIII | 1.06 | 3 | 0 | Inf | T9899C |
| 12633 | C | A | ND5 | 1.21 | 3 | 0 | Inf | C12633A |
| 12633 | C | T | ND5 | 0.28 | 3 | 0 | Inf | C12633T |
| 16163 | A | G | ATT/D-Loop/HVS1/7S DNA/TAS | 1.40 | 3 | 0 | Inf | A16163G |
| 16186 | C | T | ATT/D-Loop/HVS1/7S DNA | 1.24 | 1 | 0 | Inf | C16186T |
| 16189 | T | C | ATT/D-Loop/HVS1/7S DNA | 25.41 | 1 | 0 | Inf | T16189C |
| 16311 | T | C | ATT/D-Loop/HVS1/7S DNA | 20.66 | 1 | 1 | 1.222392 | T16311C |
Enriched in low LVSD (<-1fc)
| tpos | tnt | qnt | calc_locus | gb_perc | hot | cold | enrichment | allele |
|---|---|---|---|---|---|---|---|---|
| 194 | C | T | HVS2/OH/ATT/D-Loop | 1.73 | 0 | 1 | -Inf | C194T |
| 207 | G | A | HVS2/OH/ATT/D-Loop | 4.69 | 0 | 1 | -Inf | G207A |
| 321 | T | C | HVS2/OH/HPR/ATT/D-Loop | 0.04 | 0 | 1 | -Inf | T321C |
| 930 | G | A | 12S | 2.04 | 0 | 4 | -Inf | G930A |
| 3204 | C | T | 16S | 0.37 | 0 | 1 | -Inf | C3204T |
| 3398 | T | C | ND1 | 0.36 | 0 | 1 | -Inf | T3398C |
| 5147 | G | A | ND2 | 4.12 | 0 | 4 | -Inf | G5147A |
| 5277 | T | C | ND2 | 0.26 | 0 | 1 | -Inf | T5277C |
| 5426 | T | C | ND2 | 1.05 | 0 | 2 | -Inf | T5426C |
| 5460 | G | A | ND2 | 6.25 | 0 | 1 | -Inf | G5460A |
| 5747 | A | G | OL | 0.09 | 0 | 1 | -Inf | A5747G |
| 6489 | C | A | COI | 0.21 | 0 | 1 | -Inf | C6489A |
| 7295 | A | G | COI | 0.02 | 0 | 1 | -Inf | A7295G |
| 8537 | A | G | ATPase8/ATPase6 | 0.07 | 0 | 1 | -Inf | A8537G |
| 8572 | G | A | ATPase8/ATPase6 | 0.28 | 0 | 1 | -Inf | G8572A |
| 8854 | G | A | ATPase6 | 0.08 | 0 | 1 | -Inf | G8854A |
| 9233 | T | C | COIII | 0.13 | 0 | 1 | -Inf | T9233C |
| 11242 | C | G | ND4 | 0.06 | 0 | 1 | -Inf | C11242G |
| 11812 | A | G | ND4 | 3.30 | 0 | 7 | -Inf | A11812G |
| 12373 | A | G | ND5 | 0.15 | 0 | 1 | -Inf | A12373G |
| 13260 | T | C | ND5 | 0.21 | 0 | 1 | -Inf | T13260C |
| 13708 | G | A | ND5 | 6.82 | 0 | 1 | -Inf | G13708A |
| 14233 | A | G | ND6 | 3.66 | 0 | 7 | -Inf | A14233G |
| 15028 | C | A | Cytb | 0.20 | 0 | 1 | -Inf | C15028A |
| 15043 | G | A | Cytb | 22.77 | 0 | 1 | -Inf | G15043A |
| 16224 | T | C | ATT/D-Loop/HVS1/7S DNA | 5.00 | 0 | 1 | -Inf | T16224C |
| 16278 | C | T | ATT/D-Loop/HVS1/7S DNA | 10.27 | 0 | 1 | -Inf | C16278T |
| 16296 | C | T | ATT/D-Loop/HVS1/7S DNA | 2.25 | 0 | 1 | -Inf | C16296T |
| 16304 | T | C | ATT/D-Loop/HVS1/7S DNA | 6.57 | 0 | 1 | -Inf | T16304C |
T1 vs T2
T1 and T2, appear to segregate strongly with regard to LVSD.
The major subclades of T are distinguished by just a few loci.
T1 is defined by C12633A A16163G T16189C
T2 is defined by A11812G A14233G (C16296T)
See http://www.ncbi.nlm.nih.gov/pubmed/19434233
T subclade summary
| twoletterhaplogroup | cnt | mean | range | sd |
|---|---|---|---|---|
| T1 | 7 | 2.3571429 | 1-4 | 1.0293317 |
| T2 | 9 | 0.2777778 | 0-1.5 | 0.5651942 |
Logistic regression assuming lvsd>1 is affected
##
## Call:
## glm(formula = affected ~ twoletterhaplogroup, family = binomial(link = "logit"),
## data = Tdf)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.9728 -0.4854 -0.4854 0.5553 2.0963
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.792 1.080 1.659 0.0971 .
## twoletterhaplogroupT2 -3.871 1.514 -2.557 0.0105 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 21.930 on 15 degrees of freedom
## Residual deviance: 12.021 on 14 degrees of freedom
## AIC: 16.021
##
## Number of Fisher Scoring iterations: 4Logistic regression by the outcome variable (ignoring -9’s)
##
## Call:
## glm(formula = status ~ twoletterhaplogroup, family = binomial(link = "logit"),
## data = Tdfo)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.51678 -0.51678 -0.25837 0.00005 2.03933
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 20.57 7238.39 0.003 0.998
## twoletterhaplogroupT2 -22.51 7238.39 -0.003 0.998
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 19.4081 on 13 degrees of freedom
## Residual deviance: 6.0283 on 12 degrees of freedom
## AIC: 10.028
##
## Number of Fisher Scoring iterations: 19Next steps
- Parsable Phylotree
- Build mixed model, test at different levels (macro, two-letter, three-letter)
- Look at heteroplasmies
- Investigate burden of variants - especially in ND4 and ND6
- Develop RF or other ML approaches for classification